GROMACS version:2022.2
GROMACS modification: No
Hi Im doing Protein-NonProtein MD simulation for the first time and following the tutorial(Protein-Ligand Complex) with the same example files.
I am following the tutorial as it is but facing a few problems.
- The
"jz4.gro"gives a distorted structure (shown below). while the programgmx editconf -f jz4_ini.pdb -o jz4.grogot executed without any error.
- program for NVT equilibration got executed successfully with out any error but NPT equilibration gives warning flags and shows error. Please find the attached log below.
gmx grompp -f npt.mdp -c nvt.gro -t nvt.cpt -r nvt.gro -p topol.top -n index.ndx -o npt.tpr
Ignoring obsolete mdp entry ‘title’
** Ignoring obsolete mdp entry ‘ns_type’**
** WARNING 1 [file npt.mdp]:**
** The Berendsen barostat does not generate any strictly correct ensemble,**
** and should not be used for new production simulations (in our opinion).**
** For isotropic scaling we would recommend the C-rescale barostat that also**
** ensures fast relaxation without oscillations, and for anisotropic scaling**
** you likely want to use the Parrinello-Rahman barostat.**
** Setting the LD random seed to -672334401**
** Generated 100032 of the 100128 non-bonded parameter combinations**
** Generating 1-4 interactions: fudge = 1**
** Generated 65937 of the 100128 1-4 parameter combinations**
** Excluding 3 bonded neighbours molecule type ‘Protein_chain_A’**
** turning H bonds into constraints…**
** Excluding 3 bonded neighbours molecule type ‘JZ4’**
** turning H bonds into constraints…**
** Excluding 2 bonded neighbours molecule type ‘SOL’**
** turning H bonds into constraints…**
** Excluding 1 bonded neighbours molecule type ‘CL’**
** turning H bonds into constraints…**
** The center of mass of the position restraint coord’s is 5.887 5.889 2.782**
** The center of mass of the position restraint coord’s is 5.887 5.889 2.782**
** Number of degrees of freedom in T-Coupling group Protein_JZ4 is 6582.71**
** Number of degrees of freedom in T-Coupling group Water_and_ions is 61749.29**
** The largest distance between excluded atoms is 0.436 nm**
** Determining Verlet buffer for a tolerance of 0.005 kJ/mol/ps at 300 K**
** Calculated rlist for 1x1 atom pair-list as 1.294 nm, buffer size 0.094 nm**
** Set rlist, assuming 4x4 atom pair-list, to 1.221 nm, buffer size 0.021 nm**
** Note that mdrun will redetermine rlist based on the actual pair-list setup**
** NOTE 1 [file npt.mdp]:**
** Removing center of mass motion in the presence of position restraints**
** might cause artifacts. When you are using position restraints to**
** equilibrate a macro-molecule, the artifacts are usually negligible.**
** Reading Coordinates, Velocities and Box size from old trajectory**
** Will read whole trajectory**
** Last frame -1 time 100.000 **
** Using frame at t = 100 ps**
** Starting time for run is 0 ps**
** Calculating fourier grid dimensions for X Y Z**
** Using a fourier grid of 52x52x52, spacing 0.151 0.151 0.151**
** Estimate for the relative computational load of the PME mesh part: 0.20**
** This run will generate roughly 19 Mb of data**
** There was 1 note**
** There was 1 warning**
** -------------------------------------------------------**
** Program: gmx grompp, version 2022.2**
** Source file: src/gromacs/gmxpreprocess/grompp.cpp (line 2661)**
** Fatal error:**
** Too many warnings (1).**
** If you are sure all warnings are harmless, use the -maxwarn option.**
How to fix this error or should I ignore it? Is it possible to trace back mistakes if I have done in any of previous steps?
Thank you so much